6-157690668-C-G

Position:

• chr6-157690668-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.66 (29310 hom., cov: 18)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.461

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.685 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.663 AC: 88810 AN: 133958 Hom.: 29305 Cov.: 18

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.656

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.663 AC: 88832 AN: 134000 Hom.: 29310 Cov.: 18 AF XY: 0.665 AC XY: 42143 AN XY: 63348

Gnomad4 AFR AF: 0.627

Gnomad4 AMR AF: 0.697

Gnomad4 ASJ AF: 0.643

Gnomad4 EAS AF: 0.694

Gnomad4 SAS AF: 0.706

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.658

Alfa AF: 0.655 Hom.: 3910

Bravo AF: 0.663

Asia WGS AF: 0.708 AC: 2443 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.57

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6903041; hg19: chr6-158111700;